Hi, It depends on the details of what is in your PDB file -- sometimes you can use "ligand" to mean the ligand, and "protein" to mean the receptor, but sometimes you have to use the residue names or numbers instead. The general process is (1) use the Select menu to select the part you want (look under Select... Structure for "protein" and "ligand", under Select... Residue for residue names) (2) use Actions menu to do something to that part (for example, Actions... Color) I suggest you try the "getting started" tutorial to get some basic knowledge of Chimera: <http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 6, 2011, at 11:40 AM, Bishwajit Das wrote:

Hi I am using chimera,i am a new user of this and i open a docking model in .pdb format. Now my question is how i seen that model which is recepter and which is ligand.How i differentiate with recepter and ligand with two another colour. Please help me with step by step Thank you -- BISHWAJIT DAS KOLKATA